The River Danube is, with 2780 km, the second longest river in Europe. Its catchment area covers 801 500 km(2), with approximately 81 million inhabitants in 19 countries. River water for anthropogenic use, transportation and recreation is of major importance in all of these countries. Microbiological contamination from faecal pollution by anthropogenic sources is considered to be a crucial problem throughout the Danube River basin. Thus, detailed knowledge on the extent and the origin of microbial pollution is essential for watershed management. The determination of faecal indicator concentrations along the Danube and its major tributaries during two whole-river surveys and 16 permanent stations allowed for the first time to draw a clear picture of the faecal pollution patterns along the whole longitudinal profile of this important international river. By including a variety of environmental variables in statistical analysis, an integrative picture of faecal pollution in the Danube River basin could be evolved. Four hot spots and six stretches of differing faecal pollution were identified, mainly linked with input from large municipalities. Significant decline of microbiological pollution was observed in the upper and lower Danube stretches over the investigation period. In contrast, a significant increase in the middle part was evident. The planned implementation of new wastewater treatment plants and advanced wastewater treatment measures according to the European Union urban wastewater directive will have a great potential to reduce microbial faecal pollution in the Danube and thus improving water quality.